The DH-led performance and capability review criticised the CQC and the DH for underestimating the scale of the task of registering more than 21,000 health and social care providers across England.
The review said that the CQC could have done more to manage risks during the early years of its operation and said it had not made its role clear to health and care providers, patients and the public.
The review set out a number of recommendations for the CQC to help improve in the future. These included giving frontline inspectors ‘greater access’ to doctors and nurses, ensuring there are enough inspectors to meet future demand and making inspections more consistent.
Ms Bower said: ‘After almost four years leading CQC, I feel that it is now time to move on. The process of setting up an entirely new system of regulation has been intensely challenging - but we have accomplished an enormous amount.
‘I am pleased that the DH performance and capability review, published today, recognises the scale of what has been achieved - and in particular the significant improvements made over the last nine months.’
Ms Bower will remain in post until autumn 2012 to allow for an appropriate handover. The recruitment process for her successor will begin shortly.
A CQC spokesman said that Ms Bower’s resignation would not affect GP registration due to start in April 2013. However GPC negotaitor Dr Chaand Nagpual warned that a change in leadership could lead to a change in policy.
'This clearly does create a break. We will need to work with CQC with any successor and make sure any concerns about the registration process are heard and put forward.'